Campaign 2017 (PhD Chapter 1)

1. Maps
- 1.1. General map
- 1.2. Parameters maps
2. Figures

This series of files compile all analyses done during Chapter 1 for the regional campaign of 2017.

All analyses have been done with PRIMER-e 6 and R 3.6.0.

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Caracteristics of each campaign

		2014	2017	2017
Sampling date		August-September	June to August	July
Criteria for perturbation		Potentially impacted if close to the city or industries, References outside the bay	Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria	Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria
Regions considered		BSI	BSI, CPC, BDA, MR	BSI, MR
Number of sampled stations		40 (20 HI, 20 R)	78 (26 BSI, 19 CPC, 18 BDA, 15 MR)	126 (111 BSI, 15 MR)
Parameters sampled	Organic matter	yes	yes	yes
	Photosynthetic pigments	no	yes	yes
	Sediment grain-size	yes	yes	yes
	Heavy-metals	yes	yes (for a limited number of stations)	no (interpolated based on 2014 and 2017 values)
Benthic communities	Compartment targeted	Macro-infauna	Macro-infauna	Macro-infauna
	Sieved used	500 µm	1 mm	500 µm and 1 mm
	Conservation technique	Formaldehyle	Formaldehyle	Formaldehyle
Others		N.A.	N.A.	N.A.

We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

Depth of the station: depth (only for ANCOVAs)
Percentage of organic matter: om
Percentage of gravel: gravel
Percentage of sand: sand
Percentage of silt: silt
Percentage of clay: clay
Concentration of arsenic: arsenic
Concentration of cadmium: cadmium
Concentration of chromium: chromium
Concentration of copper: copper
Concentration of iron: iron
Concentration of manganese: manganese
Concentration of mercury: mercury
Concentration of lead: lead
Concentration of zinc: zinc
Species richness: S (only for 500 µm communities)
Abundance of total individuals: N (only for 500 µm communities)
Shannon index: H (only for 500 µm communities)
Piélou evenness: J (only for 500 µm communities)

We only considered 500 µm communities for these analyses. Abundances of Bipalponephtys neotena (Bneo) and Nematoda (Nema) were also considered (see IndVal and SIMPER results).

Heavy metal concentrations for campaign 2017 have been kriged from the values collected at campaigns 2014 and 2016. As data is missing for metal concentrations outside BSI, two Designs have been used:

Design 1: stations at BSI, MR with habitat parameters
Design 2: stations at BSI with heavy metal concentrations.

Statistics for each variable considered:

BSI, MR (without heavy metals)
	Mean	SD	SE	Median	Min	Max	95% CI
depth	22.364	18.168	2.909	20.900	1.600	66.900	5.702
om	0.885	0.726	0.116	0.620	0.186	3.872	0.228
gravel	0.028	0.115	0.018	0.000	0.000	0.701	0.036
sand	0.649	0.271	0.043	0.675	0.005	0.992	0.085
silt	0.304	0.239	0.038	0.322	0.007	0.869	0.075
clay	0.020	0.084	0.014	0.000	0.000	0.407	0.026
S_500	10.436	4.994	0.800	11.000	1.000	23.000	1.567
N_500	79.795	80.331	12.863	58.000	1.000	382.000	25.212
H_500	1.588	0.620	0.099	1.643	0.000	2.568	0.194
J_500	0.700	0.210	0.034	0.738	0.000	1.000	0.066

BSI (only heavy metals)
	Mean	SD	SE	Median	Min	Max	95% CI
arsenic	3.908	3.085	0.630	2.750	1.500	16.000	1.234
cadmium	0.150	0.041	0.008	0.145	0.090	0.230	0.017
chromium	55.163	20.949	4.276	54.750	28.000	110.700	8.381
copper	11.121	6.686	1.365	8.950	2.900	28.700	2.675
iron	49908.033	13633.036	2782.832	48883.150	28355.900	78471.300	5454.250
manganese	952.654	455.270	92.932	847.700	423.100	2098.000	182.142
mercury	0.024	0.016	0.003	0.021	0.008	0.087	0.006
lead	5.533	2.520	0.514	5.050	2.400	12.100	1.008
zinc	61.654	25.066	5.117	55.750	33.500	141.000	10.028

1. Maps

1.1. General map

1.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Species

Species richness

Total abundance

Shannon index

Piélou’s evenness

2. Figures

2.1. Barplots

Two types of barplots are available: one for the means by region, and one for the means by depth class. The latter have been done by classifying stations along three groups, based on their depth: shallow (0-10 m), medium (10-25 m) and deep (> 25 m). These thresholds are not supported by evidence, but allow to get a balanced design (26 stations for each depth class). However, we have been using PERMANOVA with depth as a covariate, instead of using these classes as a third factor.

Heavy metals are not presented here, as they were only sampled at BSI stations.

Regions

Organic matter

Grain-size

Species abundances

Diversity indices

Depth classes

Organic matter

Grain-size

Species abundances

Diversity indices

2.2. Phylum frequencies

Phylum abundances by condition
Phylum	HI	R
Arthropoda	879	81
Annelida	811	40
Mollusca	337	310
Nematoda	242	270
Echinodermata	29	104
Nemertea	4	0
Bryozoa	0	0
Chaetognatha	0	0
Cnidaria	0	3
Hemichordata	0	0
Phoronida	0	0
Platyhelminthes	0	0
Sipuncula	0	2